The mouse genome project is at an earlier stage of development than its human counterpart, despite the fact that much more is known about mouse genetics and the exciting prospect that mouse genes, once identified, can be manipulated and their function determined. One reason for the status of the mouse genome project has been the difficulty of resolving the mouse flow karyotype. Multiple approaches to this task have now been developed in the NFCR with the assistance of several collaborators. Sorting of the mouse Y chromosome has been a high priority. Mouse-Chinese hamster somatic cell hybrids containing limited numbers of mouse chromosomes have been evaluated. We have also identified the peaks of a mouse bivariate flow karyotype and we have acquired some unique cell lines containing multi-Robertsonian translocations. Single chromosome types are being sorted from high resolution bivariate flow karyotypes, amplified (using degenerate oligonucleotide primers) , and hybridized to spreads of mouse spleen cells for fluorescence in-situ hybridization techniques to identify the peaks of the flow karyotype. Mouse Robertsonian chromosomes (4;6) have been sorted and phage libraries constructed. These techniques will greatly facilitate the mouse genome project.